Improved Prediction of Protein-Protein Interactions Using Descriptors Derived From PSSM via Gray Level Co-Occurrence Matrix

Hui Juan Zhu, Zhu Hong You, Wei Lei Shi, Shou Kun Xu, Tong Hai Jiang, Li Hua Zhuang

Research output: Contribution to journalArticlepeer-review

11 Scopus citations

Abstract

A better exploring biological processes, means, and functions demands trusted information about Protein-protein interactions (PPIs). High-throughput technologies have produced a large number of PPIs data for various species, however, they are resource-expensive and often suffer from high error rates. To supplement the limitations of the traditional methods, in this paper, a sequence-based computational method is proposed to insight whether two proteins interact or not. The proposed method divides the novel PPIs prediction process into three stages: first, the position-specific scoring matrices (PSSMs) are produced by incorporating the evolutionary information; second, the 352-dimensional feature vector is constructed for each protein pair; third, effective parameters for the ensemble learning algorithm rotation forest (RF) are selected. In the proposed model, the evolutionary features are extracted from PSSM for each protein without considering any protein annotations. In addition, by using more accurate and diverse classifiers constructed by RF algorithm to avoid yielding coincident errors, one sample incorrectly divided by one classifier will be corrected by another classifier. The proposed method is evaluated in terms of accuracy, precision, sensitivity, and so on using Yeast, Human, and Pylori datasets and finds that its performance is superior to that of the competing methods. Specifically, the average accuracies achieved by the proposed method are 97.06% (Yeast), 98.95% (Human), and 89.69% (H.pylori), which improves the accuracy of PPIs prediction by 0.54%3.89% (Yeast), 1.29%3.85% (Human), and 0.22%4.85% (H.pylori). The experimental results prove that the proposed method is an effective alternative approach for predicting novel PPIs.

Original languageEnglish
Article number8673760
Pages (from-to)49456-49465
Number of pages10
JournalIEEE Access
Volume7
DOIs
StatePublished - 2019
Externally publishedYes

Keywords

  • gray level co-occurrence matrix
  • position-specific scoring matrix
  • Protein-protein interactions
  • rotation forest

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